Contacts of the helix formed by residues 112 - 125 (chain A) in PDB entry 4O5A
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP 112 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110A ASP* 4.5 1.6 - - - +
111A ASP* 1.3 76.9 - - + +
113A ASP* 1.3 63.6 + - - +
114A GLU 3.4 2.0 - - - -
115A VAL* 3.6 12.6 + - + +
116A SER* 3.4 20.3 + - - -
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Residues in contact with ASP 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A MSE 4.1 1.6 - - - +
108A SER* 3.6 17.7 - - - -
109A MSE 2.9 29.3 + - - +
110A ASP* 3.7 22.8 + - + +
111A ASP 3.3 0.4 - - - -
112A ASP* 1.3 76.4 - - - +
114A GLU* 1.3 66.1 + - - +
116A SER* 3.3 9.3 + - - -
117A ILE* 3.1 32.8 + - - +
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Residues in contact with GLU 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A VAL* 4.0 36.8 + - + +
72A LEU 6.2 0.2 - - - -
108A SER* 3.6 20.9 + - - +
110A ASP 4.8 0.2 + - - -
111A ASP 4.5 7.2 + - - +
112A ASP 3.4 0.8 - - - -
113A ASP* 1.3 79.2 - - - +
115A VAL* 1.3 64.3 + - + +
117A ILE* 3.1 4.0 + - - +
118A LEU* 2.9 38.9 + - + +
131A LEU 5.3 2.1 - - - +
132A LEU* 4.8 2.4 - - - +
141A ARG* 2.9 46.1 + - - -
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Residues in contact with VAL 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A ASP 5.5 2.2 - - - +
112A ASP* 3.6 14.9 + - + +
113A ASP 3.4 0.4 - - - -
114A GLU* 1.3 76.7 - - + +
116A SER* 1.3 57.6 + - - +
118A LEU* 3.2 9.4 + - - +
119A GLU* 2.8 57.7 + - + +
140A PRO* 4.2 34.1 - - + +
141A ARG* 4.3 15.7 - - + -
144A LEU* 4.1 12.1 - - + -
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Residues in contact with SER 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A ASP 3.4 11.1 + - - -
113A ASP* 3.3 13.6 + - - -
114A GLU 3.2 0.8 - - - -
115A VAL* 1.3 79.4 - - - +
117A ILE* 1.3 62.1 + - - +
119A GLU* 3.4 14.5 + - - +
120A ASP* 3.1 21.7 + - - +
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Residues in contact with ILE 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A VAL* 3.8 33.9 - - + -
106A ARG* 3.9 51.6 - - + +
107A MSE 3.9 20.2 - - - +
113A ASP* 3.1 30.2 + - - +
114A GLU 3.1 5.6 + - - +
116A SER* 1.3 75.6 - - - +
118A LEU* 1.3 65.0 + - - +
120A ASP* 3.1 8.9 + - + +
121A TRP* 3.0 33.5 + - + +
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Residues in contact with LEU 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A VAL* 4.0 20.2 - - + +
114A GLU* 2.9 39.9 + - + +
115A VAL 3.6 3.8 - - - +
117A ILE* 1.3 75.8 - - - +
119A GLU* 1.3 58.1 + - - +
121A TRP* 3.2 16.1 + - + +
122A ILE* 2.9 35.9 + - - +
130A LEU* 4.0 28.4 - - + +
131A LEU 5.9 1.6 - - - +
132A LEU* 4.3 12.6 - - + -
141A ARG* 3.9 24.9 - - + -
144A LEU* 3.7 17.3 - - + -
145A MSE 5.2 1.8 - - - -
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Residues in contact with GLU 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A VAL* 2.8 38.2 + - - +
116A SER* 3.7 14.4 + - - +
117A ILE 3.3 0.4 - - - -
118A LEU* 1.3 74.6 - - - +
120A ASP* 1.3 57.7 + - - +
122A ILE* 3.4 8.0 + - - +
123A ALA* 3.0 30.9 + - - +
144A LEU* 3.7 25.9 - - + +
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Residues in contact with ASP 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A ARG* 4.5 13.1 + - - +
116A SER 3.1 12.7 + - - +
117A ILE* 3.1 12.0 + - - +
119A GLU* 1.3 75.4 - - - +
121A TRP* 1.3 77.0 + - - +
123A ALA* 3.3 4.0 + - - -
124A THR* 2.9 44.8 + - - +
126A ASN* 5.7 0.2 - - - +
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Residues in contact with TRP 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A GLY* 3.4 21.8 - - - -
70A LEU 3.5 15.5 - - - -
71A VAL* 3.8 20.0 - - + -
104A LEU* 3.5 48.7 - - + +
106A ARG* 3.8 31.9 - - + +
117A ILE* 3.0 17.9 + - + +
118A LEU* 3.6 17.0 - - + +
120A ASP* 1.3 89.3 + - - +
122A ILE* 1.3 58.5 + - - +
124A THR* 3.9 2.5 - - - -
125A GLY* 2.8 25.5 + - - -
126A ASN* 3.1 27.5 + - + +
127A VAL* 4.3 15.0 - - + -
130A LEU* 3.5 22.7 - - + -
151A MSE 3.8 4.7 - - - +
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Residues in contact with ILE 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A LEU 2.9 22.0 + - - +
119A GLU* 3.7 5.6 - - - +
121A TRP* 1.3 77.2 - - - +
123A ALA* 1.3 62.5 + - - +
124A THR 3.4 0.3 + - - -
125A GLY* 3.4 9.7 + - - -
130A LEU* 4.2 6.1 - - + -
144A LEU* 4.1 31.4 - - + -
145A MSE 4.3 14.6 - - + -
148A ASN* 3.4 38.4 - - + +
150A GLN* 3.7 15.6 + - - +
151A MSE 3.9 28.2 - - + +
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Residues in contact with ALA 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A GLU 3.0 18.6 + - - +
120A ASP* 3.3 6.3 + - - +
122A ILE* 1.3 79.7 - - - +
124A THR* 1.3 64.3 + - + +
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Residues in contact with THR 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A ASP* 2.9 36.7 + - - +
121A TRP* 3.9 0.3 - - - -
123A ALA* 1.3 82.8 - - + +
125A GLY* 1.3 63.4 + - - +
126A ASN* 3.3 24.9 + - - +
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Residues in contact with GLY 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A THR* 3.4 16.6 - - - +
121A TRP 2.8 9.9 + - - -
122A ILE 3.4 8.9 + - - -
124A THR* 1.3 79.1 - - - +
126A ASN* 1.3 61.6 + - - +
127A VAL 3.2 11.7 + - - +
151A MSE 4.7 4.7 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il